diff --git a/package.json b/package.json
index 891376183..4c0e8ba97 100644
--- a/package.json
+++ b/package.json
@@ -24,7 +24,7 @@
     "atom-keymap": "^3.1.2",
     "bootstrap": "git+https://github.com/atom/bootstrap.git#6af81906189f1747fd6c93479e3d998ebe041372",
     "clear-cut": "0.4.0",
-    "coffee-cash": "0.5.0",
+    "coffee-cash": "0.6.0",
     "coffee-script": "1.8.0",
     "coffeestack": "^1.1",
     "color": "^0.7.3",
diff --git a/src/6to5.coffee b/src/6to5.coffee
index e24c63768..3ceb81480 100644
--- a/src/6to5.coffee
+++ b/src/6to5.coffee
@@ -139,15 +139,20 @@ loadFile = (module, filePath) ->
   js = getCachedJavaScript(cachePath) ? transpile(sourceCode, filePath, cachePath)
   module._compile(js, filePath)
 
-register = (newCacheDir) ->
-  cacheDir = newCacheDir
+register = ->
   Object.defineProperty(require.extensions, '.js', {
     writable: false
     value: loadFile
   })
 
+setCacheDirectory = (newCacheDir) ->
+  if cacheDir isnt newCacheDir
+    cacheDir = newCacheDir
+    jsCacheDir = null
+
 module.exports =
   register: register
+  setCacheDirectory: setCacheDirectory
   getCacheMisses: -> stats.misses
   getCacheHits: -> stats.hits
 
diff --git a/src/compile-cache.coffee b/src/compile-cache.coffee
new file mode 100644
index 000000000..d5e9f0ccf
--- /dev/null
+++ b/src/compile-cache.coffee
@@ -0,0 +1,26 @@
+path = require 'path'
+
+CSON = require 'season'
+CoffeeCache = require 'coffee-cash'
+to5 = require './6to5'
+
+cacheDir = path.join(process.env.ATOM_HOME, 'compile-cache')
+# Use separate compile cache when sudo'ing as root to avoid permission issues
+if process.env.USER is 'root' and process.env.SUDO_USER and process.env.SUDO_USER isnt process.env.USER
+  cacheDir = path.join(cacheDir, 'root')
+
+CoffeeCache.setCacheDirectory(path.join(cacheDir, 'coffee'))
+CSON.setCacheDir(path.join(cacheDir, 'cson'))
+to5.setCacheDirectory(path.join(cacheDir, 'js'))
+
+# This file is required directly by apm so that files can be cached during
+# package install so that the first package load in Atom doesn't have to
+# compile anything.
+exports.addPathToCache = (filePath) ->
+  switch path.extname(filePath)
+    when '.coffee'
+      CoffeeCache.addPathToCache(filePath)
+    when '.cson'
+      CSON.readFileSync(filePath)
+    when '.js'
+      to5.addPathToCache(filePath)
diff --git a/static/index.js b/static/index.js
index 88634ee63..ebb921100 100644
--- a/static/index.js
+++ b/static/index.js
@@ -13,7 +13,9 @@ window.onload = function() {
       }
 
       // Setup caching of .coffee files
-      require('coffee-cash').register(path.join(cacheDir, 'coffee'));
+      var CoffeeCache = require('coffee-cash');
+      CoffeeCache.setCacheDirectory(path.join(cacheDir, 'coffee'));
+      CoffeeCache.register();
 
       // Set up caching of source maps for generated stack traces
       require('coffeestack').setCacheDirectory(path.join(cacheDir, 'coffee', 'source-maps'));
@@ -22,7 +24,9 @@ window.onload = function() {
       require('season').setCacheDir(path.join(cacheDir, 'cson'));
 
       // Setup caching of .js files that start with "use 6to5"
-      require('../src/6to5').register(path.join(cacheDir, 'js'));
+      var to5 = require('../src/6to5');
+      to5.setCacheDirectory(path.join(cacheDir, 'js'));
+      to5.register();
     }
 
     // Ensure ATOM_HOME is always set before anything else is required